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1.
Inflamm Bowel Dis ; 26(9): 1306-1314, 2020 08 20.
Article in English | MEDLINE | ID: covidwho-684619

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has a direct impact on the gastrointestinal system, as up to 50% of fecal samples from coronavirus disease 2019 (COVID-19) patients contain detectable viral RNA despite a negative rhino-pharyngeal swab. This finding, together with an intestinal expression of angiotensin conversion enzyme 2 protein, suggests a possible fecal-oral transmission for SARS-CoV-2. Furthermore, gastrointestinal (GI) symptoms are common in COVID-19 patients including watery diarrhea, vomiting-particularly in children-nausea, and abdominal pain. Pathogenesis of SARS-CoV-2 infection presents significant similarities to those of some immune-mediated diseases, such as inflammatory bowel diseases or rheumatoid arthritis, leading to the hypothesis that targeted therapies used for the treatment of immune-mediated disease could be effective to treat (and possibly prevent) the main complications of COVID-19. In this review, we synthesize the present and future impact of SARS-CoV-2 infection on the gastrointestinal system and on gastroenterology practice, hypothesizing a potential role of the "gut-lung axis" and perhaps of the gut and lung microbiota into the interindividual differential susceptibility to COVID-19 19 disease. Finally, we speculate on the reorganization of outpatient gastroenterology services, which need to consider, among other factors, the major psychological impact of strict lockdown measures on the whole population.


Subject(s)
Betacoronavirus , Coronavirus Infections/complications , Gastrointestinal Diseases/virology , Pneumonia, Viral/complications , Coronavirus Infections/virology , Feces/virology , Gastrointestinal Tract/virology , Humans , Pandemics , Pneumonia, Viral/virology , RNA, Viral/analysis
2.
J Clin Microbiol ; 58(9)2020 08 24.
Article in English | MEDLINE | ID: covidwho-636249

ABSTRACT

The clinical performances of six molecular diagnostic tests and a rapid antigen test for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were clinically evaluated for the diagnosis of coronavirus disease 2019 (COVID-19) in self-collected saliva. Saliva samples from 103 patients with laboratory-confirmed COVID-19 (15 asymptomatic and 88 symptomatic) were collected on the day of hospital admission. SARS-CoV-2 RNA in saliva was detected using a quantitative reverse transcription-PCR (RT-qPCR) laboratory-developed test (LDT), a cobas SARS-CoV-2 high-throughput system, three direct RT-qPCR kits, and reverse transcription-loop-mediated isothermal amplification (RT-LAMP). The viral antigen was detected by a rapid antigen immunochromatographic assay. Of the 103 samples, viral RNA was detected in 50.5 to 81.6% of the specimens by molecular diagnostic tests, and an antigen was detected in 11.7% of the specimens by the rapid antigen test. Viral RNA was detected at significantly higher percentages (65.6 to 93.4%) in specimens collected within 9 days of symptom onset than in specimens collected after at least 10 days of symptoms (22.2 to 66.7%) and in specimens collected from asymptomatic patients (40.0 to 66.7%). Self-collected saliva is an alternative specimen option for diagnosing COVID-19. The RT-qPCR LDT, a cobas SARS-CoV-2 high-throughput system, direct RT-qPCR kits (except for one commercial kit), and RT-LAMP showed sufficient sensitivities in clinical use to be selectively used in clinical settings and facilities. The rapid antigen test alone is not recommended for an initial COVID-19 diagnosis because of its low sensitivity.


Subject(s)
Clinical Laboratory Techniques , Coronavirus Infections/diagnosis , Immunoassay , Nucleic Acid Amplification Techniques , Pneumonia, Viral/diagnosis , Saliva/virology , Adolescent , Adult , Aged , Aged, 80 and over , Antigens, Viral/analysis , Betacoronavirus/genetics , Betacoronavirus/isolation & purification , Clinical Laboratory Techniques/methods , Clinical Laboratory Techniques/standards , Clinical Laboratory Techniques/statistics & numerical data , Female , Humans , Immunoassay/methods , Immunoassay/standards , Immunoassay/statistics & numerical data , Male , Middle Aged , Nucleic Acid Amplification Techniques/methods , Nucleic Acid Amplification Techniques/standards , Nucleic Acid Amplification Techniques/statistics & numerical data , Pandemics , RNA, Viral/analysis , RNA, Viral/genetics , Sensitivity and Specificity , Specimen Handling , Young Adult
3.
J Clin Microbiol ; 58(9)2020 08 24.
Article in English | MEDLINE | ID: covidwho-751568

ABSTRACT

The clinical performances of six molecular diagnostic tests and a rapid antigen test for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were clinically evaluated for the diagnosis of coronavirus disease 2019 (COVID-19) in self-collected saliva. Saliva samples from 103 patients with laboratory-confirmed COVID-19 (15 asymptomatic and 88 symptomatic) were collected on the day of hospital admission. SARS-CoV-2 RNA in saliva was detected using a quantitative reverse transcription-PCR (RT-qPCR) laboratory-developed test (LDT), a cobas SARS-CoV-2 high-throughput system, three direct RT-qPCR kits, and reverse transcription-loop-mediated isothermal amplification (RT-LAMP). The viral antigen was detected by a rapid antigen immunochromatographic assay. Of the 103 samples, viral RNA was detected in 50.5 to 81.6% of the specimens by molecular diagnostic tests, and an antigen was detected in 11.7% of the specimens by the rapid antigen test. Viral RNA was detected at significantly higher percentages (65.6 to 93.4%) in specimens collected within 9 days of symptom onset than in specimens collected after at least 10 days of symptoms (22.2 to 66.7%) and in specimens collected from asymptomatic patients (40.0 to 66.7%). Self-collected saliva is an alternative specimen option for diagnosing COVID-19. The RT-qPCR LDT, a cobas SARS-CoV-2 high-throughput system, direct RT-qPCR kits (except for one commercial kit), and RT-LAMP showed sufficient sensitivities in clinical use to be selectively used in clinical settings and facilities. The rapid antigen test alone is not recommended for an initial COVID-19 diagnosis because of its low sensitivity.


Subject(s)
Clinical Laboratory Techniques , Coronavirus Infections/diagnosis , Immunoassay , Nucleic Acid Amplification Techniques , Pneumonia, Viral/diagnosis , Saliva/virology , Adolescent , Adult , Aged , Aged, 80 and over , Antigens, Viral/analysis , Betacoronavirus/genetics , Betacoronavirus/isolation & purification , Clinical Laboratory Techniques/methods , Clinical Laboratory Techniques/standards , Clinical Laboratory Techniques/statistics & numerical data , Female , Humans , Immunoassay/methods , Immunoassay/standards , Immunoassay/statistics & numerical data , Male , Middle Aged , Nucleic Acid Amplification Techniques/methods , Nucleic Acid Amplification Techniques/standards , Nucleic Acid Amplification Techniques/statistics & numerical data , Pandemics , RNA, Viral/analysis , RNA, Viral/genetics , Sensitivity and Specificity , Specimen Handling , Young Adult
4.
Mymensingh Med J ; 29(3): 596-600, 2020 Jul.
Article in English | MEDLINE | ID: covidwho-746340

ABSTRACT

There is a new public health problem around the world with the emergence and spread of 2019 novel corona virus (2019-nCoV). The disease "coronavirus disease 2019" (COVID-19) was caused by SARS-CoV-2. As virus isolates are unavailable so the public laboratories are now facing a challenge for detecting the virus because there is growing evidence of the outbreak which is more widespread than initially thought. We aimed here to discuss about the current diagnostic methodology for detecting the SARS-CoV-2 in health laboratories. Here we use the Novel Corona virus (2019-nCoV) Nucleic Acid Diagnostic Kit (PCR-Fluorescence Probing) which is a real time reverse transcription polymerase chain reaction (rRT-PCR) test. A total of 230 samples in the department of microbiology, Mymensingh Medical College from 1st, April 2020 were selected for this study. Among them 20(8.69%) were positive for SARS CoV-2 and remaining were negative. Among the positive samples 55% could amplify both the ORF 1ab and N genes. The single gene ORF 1ab or N was positive in 15% and 30% cases respectively. The Ct values (<38) of ORF 1ab gene indicated by FAM dye was 92.8% and N gene curve indicated by ROX dye was 100%. The presence of IC gene curve with Ct values (<38) indicated by CY5 dye among the positives were 70% and 100% in negatives. The Ct values (38-40) of IC (CY5) among the positives were 15%. The present study demonstrates the enormous response capacity of the study kit for detecting SARS-CoV-2 within the laboratories in Bangladesh.


Subject(s)
Coronavirus Infections/diagnosis , Coronavirus/genetics , Coronavirus/isolation & purification , Pandemics , Pneumonia, Viral/diagnosis , Real-Time Polymerase Chain Reaction/methods , Bangladesh , Betacoronavirus , Clinical Laboratory Techniques/methods , Coronavirus Infections/epidemiology , Humans , Pneumonia, Viral/epidemiology , RNA, Viral/analysis
5.
J Zhejiang Univ Sci B ; 21(9): 749-751, 2020.
Article in English | MEDLINE | ID: covidwho-745668

ABSTRACT

Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was found initially in Wuhan, China in early December 2019. The pandemic has spread to 216 countries and regions, infecting more than 23310 000 people and causing over 800 000 deaths globally by Aug. 24, 2020, according to World Health Organization (https://www.who.int/emergencies/diseases/ novel-coronavirus-2019). Fever, cough, and dyspnea are the three common symptoms of the condition, whereas the conventional transmission route for SARS-CoV-2 is through droplets entering the respiratory tract. To date, infection control measures for COVID-19 have been focusing on the involvement of the respiratory system. However, ignoring potential faecal transmission and the gastrointestinal involvement of SARS-CoV-2 may result in mistakes in attempts to control the pandemic.


Subject(s)
Betacoronavirus/isolation & purification , Coronavirus Infections/transmission , Coronavirus Infections/virology , Feces/virology , Gastrointestinal Diseases/virology , Pneumonia, Viral/transmission , Pneumonia, Viral/virology , Betacoronavirus/genetics , China/epidemiology , Coronavirus Infections/epidemiology , Environmental Microbiology , Humans , Models, Biological , Pandemics , Pneumonia, Viral/epidemiology , RNA, Viral/analysis , RNA, Viral/genetics , Virus Shedding
6.
BMC Infect Dis ; 20(1): 644, 2020 Sep 01.
Article in English | MEDLINE | ID: covidwho-740367

ABSTRACT

BACKGROUND: To explore the clinical features and CT findings of clinically cured coronavirus disease 2019 (COVID-19) patients with viral RNA positive anal swab results after discharge. METHODS: Forty-two patients with COVID-19 who were admitted to Yongzhou Central Hospital, Hunan, China, between January 20, 2020, and March 2, 2020, were tested for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using anal swab viral RT-PCR. In this report, we present the clinical characteristics and chest CT features of six patients with positive anal swab results and compare the clinical, laboratory, and CT findings between the positive and negative groups. RESULTS: The anal swab positivity rate for SARS-CoV-2 RNA in discharged patients was 14.3% (6/42). All six patients were male. In the positive group, 40% of the patients (2/5) had a positive stool occult blood test (OBT), but none had diarrhea. The median duration of fever and major symptoms (except fever) in the positive patients was shorter than that of the negative patients (1 day vs. 6 days, 4.5 days vs. 10.5 days, respectively). The incidence of asymptomatic cases in the positive group (33.3%) was also higher than that of the negative group (5.6%). There were no significant differences in the CT manifestation or evolution of the pulmonary lesions between the two groups. CONCLUSION: In our case series, patients with viral RNA positive anal swabs did not exhibit gastrointestinal symptoms, and their main symptoms disappeared early. They had similar CT features to the negative patients, which may be easier to be ignored. A positive OBT may indicate gastrointestinal damage caused by SARS-CoV-2 infection.


Subject(s)
Betacoronavirus/isolation & purification , Coronavirus Infections/diagnostic imaging , Patient Discharge/statistics & numerical data , Pneumonia, Viral/diagnostic imaging , RNA, Viral/analysis , Severe Acute Respiratory Syndrome/diagnostic imaging , Adolescent , Adult , Aged , Anal Canal/virology , Betacoronavirus/genetics , Child , Child, Preschool , China/epidemiology , Coronavirus Infections/epidemiology , Coronavirus Infections/virology , Fever , Hospitalization , Hospitals , Humans , Male , Middle Aged , Pandemics , Pneumonia, Viral/epidemiology , Pneumonia, Viral/virology , Reverse Transcriptase Polymerase Chain Reaction , Severe Acute Respiratory Syndrome/epidemiology , Severe Acute Respiratory Syndrome/virology , Tomography, X-Ray Computed , Young Adult
7.
Ocul Immunol Inflamm ; 28(6): 916-921, 2020 Aug 17.
Article in English | MEDLINE | ID: covidwho-737751

ABSTRACT

PURPOSES: To describe the prevalence of ocular features among COVID-19 patients and their relationship with clinical data, inflammatory markers and respiratory support therapy (including CPAP); to investigate SARS-CoV-2 in ocular secretions of symptomatic patients. METHODS: 172 COVID-19 patients were evaluated for presence of ocular manifestations. Clinical and laboratory data were also reviewed. Conjunctival swabs were analyzed for SARS-CoV-2 by RT-PCR. RESULTS: Forty-five patients (26.2%) reported ocular manifestations. Patients treated with CPAP were more likely to have ocular abnormalities (p <.01). The presence of ocular symptoms was not associated with more significant alterations on blood tests. Conjunctival swabs from patients with suspect conjunctivitis yielded negative results for SARS-CoV-2. CONCLUSIONS: Ocular features are not infrequent in COVID-19 patients, but the presence of SARS-CoV-2 in ocular secretions is low. Ocular manifestations in hospitalized COVID-19 patients can also be a consequence of respiratory support therapy. Prevention of possible transmission through ocular secretions is still recommended.


Subject(s)
Betacoronavirus/genetics , Conjunctiva/virology , Conjunctivitis, Viral/etiology , Coronavirus Infections/complications , Pandemics , Pneumonia, Viral/complications , RNA, Viral/analysis , Conjunctivitis, Viral/diagnosis , Conjunctivitis, Viral/virology , Coronavirus Infections/epidemiology , Cross-Sectional Studies , Female , Humans , Male , Middle Aged , Pneumonia, Viral/epidemiology
8.
J Diabetes Res ; 2020: 1652403, 2020.
Article in English | MEDLINE | ID: covidwho-733124

ABSTRACT

Background: Since December 2019, novel coronavirus- (SARS-CoV-2) infected pneumonia (COVID-19) has rapidly spread throughout China. This study is aimed at describing the characteristics of COVID-19 patients in Wuhan. Methods: 199 COVID-19 patients were admitted to Wuhan Red Cross Hospital in China from January 24th to March 15th. The cases were divided into diabetic and nondiabetic groups according to the history of taking antidiabetic drugs or by plasma fasting blood glucose level at admission, and the difference between groups were compared. Results: Among 199 COVID-19 patients, 76 were diabetic and 123 were nondiabetic. Compared with nondiabetics, patients with diabetes had an older age, high levels of fasting plasma glucose (FPG), D-dimer, white blood cell, blood urea nitrogen (BUN) and total bilirubin (TBIL), lower levels of lymphocyte, albumin and oxygen saturation (SaO2), and higher mortality (P < 0.05). The two groups showed no difference in clinical symptoms. Diabetes, higher level of D-dimer at admission, and lymphocyte count less than 0.6 × 109/L at admission were associated with increasing odds of death. Antidiabetic drugs were associated with decreasing odds of death. Treatment with low molecular weight heparin was not related to odds of death. Conclusion: The mortality rate of COVID-19 patients with diabetes was significantly higher than those without diabetes. Diabetes, higher level of D-dimer, and lymphocyte count less than 0.6 × 109/L at admission were the risk factors associated with in-hospital death.


Subject(s)
Coronavirus Infections/complications , Coronavirus Infections/mortality , Diabetes Complications/mortality , Diabetes Mellitus/mortality , Pneumonia, Viral/complications , Pneumonia, Viral/mortality , Aged , Betacoronavirus/genetics , Betacoronavirus/isolation & purification , Case-Control Studies , China/epidemiology , Clinical Laboratory Techniques/methods , Comorbidity , Coronavirus Infections/blood , Coronavirus Infections/diagnosis , Diabetes Complications/blood , Diabetes Complications/drug therapy , Diabetes Complications/epidemiology , Diabetes Mellitus/blood , Diabetes Mellitus/drug therapy , Diabetes Mellitus/epidemiology , Female , Hospital Mortality , Humans , Hypoglycemic Agents/therapeutic use , Length of Stay/statistics & numerical data , Male , Middle Aged , Pandemics , Patient Admission/statistics & numerical data , Pneumonia, Viral/blood , Pneumonia, Viral/diagnosis , RNA, Viral/analysis , Retrospective Studies , Risk Factors
9.
Front Cell Infect Microbiol ; 10: 445, 2020.
Article in English | MEDLINE | ID: covidwho-732914

ABSTRACT

A new type of coronavirus-induced pneumonia eventually termed "coronavirus disease 2019" (COVID-19) was diagnosed in patients in Wuhan (Hubei Province, China) in December 2019, and soon spread worldwide. To improve the detection rate of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), we analyzed the results of viral nucleic acid and serum-specific antibody tests on clinical samples from 20 patients with SARS-CoV-2 infection diagnosed at the First Affiliated Hospital of Guangzhou Medical University in China. By comparing various sample types collected from COVID-19 patients, we revealed multiple pathways for SARS-CoV-2 shedding, and a prolonged detectable period for viral nucleic acid test in sputum specimens, demonstrating that the timeline of the viral shedding is of great value in determining the time of release from quarantine or discharge from hospital. We also recommend for the application of serological test to assist in confirming SARS-CoV-2 infection judged by viral nucleic acid test, especially when COVID-19-related symptoms have appeared and the viral nucleic acid test was negative. Our findings are critical for the diagnosis of SARS-CoV-2 infection and for determining deadline of restriction measures to prevent transmission caused by convalescent patients with COVID-19.


Subject(s)
Betacoronavirus/isolation & purification , Clinical Laboratory Techniques , Coronavirus Infections/diagnosis , Feces/virology , Immunoglobulin G/blood , Immunoglobulin M/blood , Pneumonia, Viral/diagnosis , Sputum/virology , Antibodies, Viral/blood , Betacoronavirus/genetics , Betacoronavirus/physiology , Female , Humans , Male , Middle Aged , Pandemics , RNA, Viral/analysis , Reverse Transcriptase Polymerase Chain Reaction , Sensitivity and Specificity , Serologic Tests , Virus Shedding
10.
J Int Med Res ; 48(8): 300060520949067, 2020 Aug.
Article in English | MEDLINE | ID: covidwho-729470

ABSTRACT

The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleic acid test is currently the gold standard for diagnosing coronavirus disease 2019 (COVID-19). This disease requires high-quality viral nucleic acid tests, and selecting the type of specimen from patients, who are at different disease stages, to use in the nucleic acid test is challenging. This article reports in detail the diagnosis and treatment process for two patients with confirmed COVID-19 and analyzes the results of the SARS-CoV-2 nucleic acid tests that were used for different types of specimens (sputum from deep cough, nasopharyngeal swab, and feces). The nucleic acid testing results of sputum from deep cough showed the best performance for positive detection. Our findings provide a reference for selecting the most suitable specimen for the clinical diagnosis of COVID-19 and improving the positive detection rate.


Subject(s)
Betacoronavirus/genetics , Coronavirus Infections/diagnosis , Molecular Diagnostic Techniques/methods , Pneumonia, Viral/diagnosis , Aged , Humans , Male , Middle Aged , Pandemics , RNA, Viral/analysis
11.
J Infect Dev Ctries ; 14(7): 679-684, 2020 07 31.
Article in English | MEDLINE | ID: covidwho-721535

ABSTRACT

INTRODUCTION: Due to the coronavirus pandemic, identifying the infected individuals has become key to limiting its spread. Virus nucleic acid real-time RT-PCR testing has become the current standard diagnostic method but high demand could lead to shortages. Therefore, we propose a detection strategy using a one-step nested RT-PCR. METHODOLOGY: The nucleotide region in the ORF1ab gene that has the greatest differences between the human coronavirus and the bat coronavirus was selected. Primers were designed after that sequence. All diagnostic primers are species-specific since the 3´ end of the sequence differs from that of other species. A primer set also creates a synthetic positive control. Amplified products were seen in a 2.5% agarose gel, as well as in an SYBR Green-Based Real-Time RT-PCR. RESULTS: Amplification was achieved for the positive control and specific regions in both techniques. CONCLUSIONS: This new technique is flexible and easy to implement. It does not require a real-time thermocycler and can be interpreted in agarose gels, as well as adapted to quantify the viral genome. It has the advantage that if the coronavirus mutates in one of the key amplification nucleotides, at least one pair can still amplify, thanks to the four diagnostic primers.


Subject(s)
Betacoronavirus , Coronavirus Infections/diagnosis , Pneumonia, Viral/diagnosis , RNA, Viral/analysis , Real-Time Polymerase Chain Reaction/methods , Clinical Laboratory Techniques , Humans , Pandemics
12.
Euro Surveill ; 25(32)2020 Aug.
Article in English | MEDLINE | ID: covidwho-721443

ABSTRACT

We show the distribution of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genetic clades over time and between countries and outline potential genomic surveillance objectives. We applied three genomic nomenclature systems to all sequence data from the World Health Organization European Region available until 10 July 2020. We highlight the importance of real-time sequencing and data dissemination in a pandemic situation, compare the nomenclatures and lay a foundation for future European genomic surveillance of SARS-CoV-2.


Subject(s)
Betacoronavirus/genetics , Coronavirus Infections/epidemiology , Coronavirus/genetics , Genome, Viral/genetics , Pandemics , Pneumonia, Viral/epidemiology , RNA Replicase/genetics , RNA, Viral/analysis , Base Sequence , Betacoronavirus/pathogenicity , Coronavirus/isolation & purification , Coronavirus Infections/virology , Europe/epidemiology , Humans , Phylogeography , Pneumonia, Viral/virology , RNA, Viral/genetics , Severe Acute Respiratory Syndrome , Spatio-Temporal Analysis , World Health Organization
13.
Curr Med Sci ; 40(4): 614-617, 2020 Aug.
Article in English | MEDLINE | ID: covidwho-696956

ABSTRACT

The novel Coronavirus SARS-CoV-2 caused an outbreak of pneumonia in Wuhan, Hubei province of China in January 2020. This study aims to investigate the effects of different temperature and time durations of virus inactivation on the results of PCR testing for SARS-CoV-2. Twelve patients at the Renmin Hospital of Wuhan University suspected of being infected with SARS-CoV-2 were selected on February 13, 2020 and throat swabs were taken. The swabs were stored at room temperature (20-25°C), then divided into aliquots and subjected to different temperature for different periods in order to inactivate the viruses (56°C for 30, 45, 60 min; 65, 70, 80°C for 10, 15, 20 min). Control aliquots were stored at room temperature for 60 min. Then all aliquots were tested in a real-time fluorescence PCR using primers against SARS-CoV-2. Regardless of inactivation temperature and time, 7 of 12 cases (58.3%) tested were positive for SARS-CoV-2 by PCR, and cycle threshold values were similar. These results suggest that virus inactivation parameters exert minimal influence on PCR test results. Inactivation at 65°C for 10 min may be sufficient to ensure safe, reliable testing.


Subject(s)
Betacoronavirus/genetics , Betacoronavirus/isolation & purification , Clinical Laboratory Techniques/methods , Coronavirus Infections/diagnosis , Coronavirus Infections/virology , Pneumonia, Viral/diagnosis , Pneumonia, Viral/virology , Real-Time Polymerase Chain Reaction/methods , Virus Inactivation , Adult , Aged , China/epidemiology , Coronavirus Infections/epidemiology , Humans , Infection Control/methods , Medical Laboratory Personnel , Middle Aged , Molecular Diagnostic Techniques/methods , Occupational Exposure/prevention & control , Pandemics , Pneumonia, Viral/epidemiology , RNA, Viral/analysis , RNA, Viral/genetics , Temperature , Time Factors
14.
PLoS One ; 15(8): e0237127, 2020.
Article in English | MEDLINE | ID: covidwho-695633

ABSTRACT

BACKGROUND: The global pandemic of Severe Acute Respiratory Syndrome-Related Coronavirus 2 (SARS-CoV2) has resulted in unprecedented challenges for healthcare systems. One barrier to widespread testing has been a paucity of traditional respiratory viral swab collection kits relative to the demand. Whether other sample collection kits, such as widely available MRSA nasal swabs can be used to detect SARS-CoV-2 is unknown. METHODS: We compared simultaneous nasal MRSA swabs (COPAN ESwabs ® 480C flocked nasal swab in 1mL of liquid Amies medium) and virals wabs (BD H192(07) flexible mini-tip flocked nasopharyngeal swabs in 3mL Universal Transport Medium) for SARS-CoV-2 PCR testing using Simplexa COVID-19 Direct assay on patients over a 4-day period. When the results were discordant, the viral swab sample was run again on the Cepheid Xpert Xpress ® SARS-CoV-2 assay. RESULTS: Of the 81 included samples, there were 19 positives and 62 negatives in viral media and 18 positives and 63 negative in the MRSA swabs. Amongst all included samples, there was concordance between the COPAN ESwabs ® 480C and the viral swabs in 78 (96.3%). CONCLUSION: We found a high rate of concordance in test results between COPAN ESwabs ® 480C in Amies solution and BD H192(07) nasopharyngeal swabs in in 3 mL of Universal Viral Transport medium viral media. Clinicians and laboratories should feel better informed and assured using COPAN ESwabs ® 480C to help in the diagnosis of COVID-19.


Subject(s)
Betacoronavirus/genetics , Coronavirus Infections/diagnosis , Methicillin-Resistant Staphylococcus aureus/genetics , Pneumonia, Viral/diagnosis , Specimen Handling/methods , Betacoronavirus/isolation & purification , Coronavirus Infections/virology , Humans , Methicillin-Resistant Staphylococcus aureus/isolation & purification , Nasopharynx/microbiology , Nasopharynx/virology , Pandemics , Pneumonia, Viral/virology , RNA Stability , RNA, Bacterial/analysis , RNA, Bacterial/metabolism , RNA, Viral/analysis , RNA, Viral/metabolism , Real-Time Polymerase Chain Reaction
15.
Int J Mol Sci ; 21(15)2020 Jul 29.
Article in English | MEDLINE | ID: covidwho-693630

ABSTRACT

To control the COVID-19 pandemic and prevent its resurgence in areas preparing for a return of economic activities, a method for a rapid, simple, and inexpensive point-of-care diagnosis and mass screening is urgently needed. We developed and evaluated a one-step colorimetric reverse-transcriptional loop-mediated isothermal amplification assay (COVID-19-LAMP) for detection of SARS-CoV-2, using SARS-CoV-2 isolate and respiratory samples from patients with COVID-19 (n = 223) and other respiratory virus infections (n = 143). The assay involves simple equipment and techniques and low cost, without the need for expensive qPCR machines, and the result, indicated by color change, is easily interpreted by naked eyes. COVID-19-LAMP can detect SARS-CoV-2 RNA with detection limit of 42 copies/reaction. Of 223 respiratory samples positive for SARS-CoV-2 by qRT-PCR, 212 and 219 were positive by COVID-19-LAMP at 60 and 90 min (sensitivities of 95.07% and 98.21%) respectively, with the highest sensitivities among nasopharyngeal swabs (96.88% and 98.96%), compared to sputum/deep throat saliva samples (94.03% and 97.02%), and throat swab samples (93.33% and 98.33%). None of the 143 samples with other respiratory viruses were positive by COVID-19-LAMP, showing 100% specificity. Samples with higher viral load showed shorter detection time, some as early as 30 min. This inexpensive, highly sensitive and specific COVID-19-LAMP assay can be useful for rapid deployment as mobile diagnostic units to resource-limiting areas for point-of-care diagnosis, and for unlimited high-throughput mass screening at borders to reduce cross-regional transmission.


Subject(s)
Betacoronavirus/genetics , Colorimetry/methods , Coronavirus Infections/diagnosis , Mass Screening/economics , Pneumonia, Viral/diagnosis , RNA, Viral/analysis , Betacoronavirus/isolation & purification , Colorimetry/economics , Coronavirus Infections/virology , Humans , Limit of Detection , Nasopharynx/virology , Nucleic Acid Amplification Techniques/methods , Pandemics , Pneumonia, Viral/virology , Point-of-Care Systems , RNA, Viral/metabolism , Viral Load
16.
Int J Mol Sci ; 21(15)2020 Aug 04.
Article in English | MEDLINE | ID: covidwho-693534

ABSTRACT

The current COronaVIrus Disease 2019 (COVID-19) pandemic started in December 2019. COVID-19 cases are confirmed by the detection of SARS-CoV-2 RNA in biological samples by RT-qPCR. However, limited numbers of SARS-CoV-2 genomes were available when the first RT-qPCR methods were developed in January 2020 for initial in silico specificity evaluation and to verify whether the targeted loci are highly conserved. Now that more whole genome data have become available, we used the bioinformatics tool SCREENED and a total of 4755 publicly available SARS-CoV-2 genomes, downloaded at two different time points, to evaluate the specificity of 12 RT-qPCR tests (consisting of a total of 30 primers and probe sets) used for SARS-CoV-2 detection and the impact of the virus' genetic evolution on four of them. The exclusivity of these methods was also assessed using the human reference genome and 2624 closely related other respiratory viral genomes. The specificity of the assays was generally good and stable over time. An exception is the first method developed by the China Center for Disease Control and prevention (CDC), which exhibits three primer mismatches present in 358 SARS-CoV-2 genomes sequenced mainly in Europe from February 2020 onwards. The best results were obtained for the assay of Chan et al. (2020) targeting the gene coding for the spiking protein (S). This demonstrates that our user-friendly strategy can be used for a first in silico specificity evaluation of future RT-qPCR tests, as well as verifying that the former methods are still capable of detecting circulating SARS-CoV-2 variants.


Subject(s)
Betacoronavirus/genetics , Coronavirus Infections/diagnosis , Genome, Viral , Pneumonia, Viral/diagnosis , RNA, Viral/metabolism , Real-Time Polymerase Chain Reaction/methods , Betacoronavirus/isolation & purification , Coronavirus Infections/virology , Databases, Genetic , Humans , Open Reading Frames/genetics , Pandemics , Pneumonia, Viral/virology , Polymorphism, Single Nucleotide , RNA Replicase/genetics , RNA, Viral/analysis , Sensitivity and Specificity , Whole Genome Sequencing
17.
Sensors (Basel) ; 20(15)2020 Jul 31.
Article in English | MEDLINE | ID: covidwho-693345

ABSTRACT

Coronaviruses have received global concern since 2003, when an outbreak caused by SARS-CoV emerged in China. Later on, in 2012, the Middle-East respiratory syndrome spread in Saudi Arabia, caused by MERS-CoV. Currently, the global crisis is caused by the pandemic SARS-CoV-2, which belongs to the same lineage of SARS-CoV. In response to the urgent need of diagnostic tools, several lab-based and biosensing techniques have been proposed so far. Five main areas have been individuated and discussed in terms of their strengths and weaknesses. The cell-culture detection and the microneutralization tests are still considered highly reliable methods. The genetic screening, featuring the well-established Real-time polymerase chain reaction (RT-PCR), represents the gold standard for virus detection in nasopharyngeal swabs. On the other side, immunoassays were developed, either by screening/antigen recognition of IgM/IgG or by detecting the whole virus, in blood and sera. Next, proteomic mass-spectrometry (MS)-based methodologies have also been proposed for the analysis of swab samples. Finally, virus-biosensing devices were efficiently designed. Both electrochemical immunosensors and eye-based technologies have been described, showing detection times lower than 10 min after swab introduction. Alternative to swab-based techniques, lateral flow point-of-care immunoassays are already commercially available for the analysis of blood samples. Such biosensing devices hold the advantage of being portable for on-site testing in hospitals, airports, and hotspots, virtually without any sample treatment or complicated lab precautions.


Subject(s)
Coronavirus Infections/diagnosis , Pneumonia, Viral/diagnosis , Point-of-Care Systems , Antibodies, Viral/blood , Betacoronavirus/genetics , Betacoronavirus/isolation & purification , Betacoronavirus/metabolism , Biosensing Techniques/methods , Coronavirus Infections/virology , Humans , Immunoassay/methods , Pandemics , Pneumonia, Viral/virology , Proteomics/methods , RNA, Viral/analysis , RNA, Viral/metabolism , Real-Time Polymerase Chain Reaction/methods
18.
Viruses ; 12(8)2020 08 04.
Article in English | MEDLINE | ID: covidwho-693300

ABSTRACT

BACKGROUND: Amplification of viral ribonucleic acid (RNA) by real-time reverse transcriptase polymerase chain reaction (rRT-PCR) is the gold standard to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Since the initial outbreak, strategies to detect and isolate patients have been important to avoid uncontrolled viral spread. Although testing capacities have been upscaled, there is still a need for reliable high throughput test systems, specifically those that require alternative consumables. Therefore, we tested and compared two different methods for the detection of viral PCR products: rRT-PCR and mass spectrometry (MS). METHODS: Viral RNA was isolated and amplified from oro- or nasopharyngeal swabs. A total of 22 samples that tested positive and 22 samples that tested negative for SARS-CoV-2 by rRT-PCR were analyzed by MS. Results of the rRT-PCR and the MS protocol were compared. RESULTS: Results of rRT-PCR and the MS test system were in concordance in all samples. Time-to-results was faster for rRT-PCR. Hands-on-time was comparable in both assays. CONCLUSIONS: MS is a fast, reliable and cost-effective alternative for the detection of SARS-CoV-2 from oral and nasopharyngeal swabs.


Subject(s)
Betacoronavirus/isolation & purification , Coronavirus Infections/diagnosis , Mass Spectrometry/methods , Pneumonia, Viral/diagnosis , Adolescent , Adult , Aged , Aged, 80 and over , Child , Coronavirus Infections/virology , Female , Humans , Male , Middle Aged , Pandemics , Pneumonia, Viral/virology , RNA, Viral/analysis , Real-Time Polymerase Chain Reaction , Time Factors , Young Adult
19.
JCI Insight ; 5(10)2020 05 21.
Article in English | MEDLINE | ID: covidwho-687860

ABSTRACT

BACKGROUNDThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a novel viral pneumonia (COVID-19), which is rapidly spreading throughout the world. The positive result of nucleic acid test is a golden criterion to confirm SARS-CoV-2 infection, but the detection features remain unclear.METHODSWe performed a retrospective analysis in 5630 high-risk individuals receiving SARS-CoV-2 nucleic acid tests in Wuhan, China, and investigated their characteristics and diagnosis rates.RESULTSThe overall diagnosis rate was 34.7% (1952/5630). Male (P = 0.025) and older populations (P = 2.525 × 10-39) were at significantly higher risk of SARS-CoV-2 infection. People were generally susceptible, and most cases concentrated in people of 30-79 years. Furthermore, we investigated the association between diagnosis rate and the amount of testing in 501 subjects. Results revealed a 1.27-fold improvement (from 27.9% to 35.5%) of diagnosis rate from testing once to twice (P = 5.847 × 10-9) and a 1.43-fold improvement (from 27.9% to 39.9%) from testing once to 3 times (P = 7.797 × 10-14). More than 3 testing administrations was not helpful for further improvement. However, this improvement was not observed in subjects with pneumonia (P = 0.097).CONCLUSIONAll populations are susceptible to SARS-CoV-2 infection, and male and older-aged populations are at significantly higher risk. Increasing the amount of testing could significantly improve diagnosis rates, except for subjects with pneumonia. It is recommended to test twice in those high-risk individuals whose results are negative the first time, and performing 3 tests is better, if possible.FUNDINGThis work was supported by National Mega Project on Major Infectious Disease Prevention (no. 2017ZX10103005-007) and National Key Research and Development Program of China (no. 2018YFE0204500).


Subject(s)
Clinical Laboratory Techniques , Coronavirus Infections/diagnosis , Pneumonia, Viral/diagnosis , Adolescent , Adult , Age Factors , Aged , Aged, 80 and over , Child , Child, Preschool , China/epidemiology , Clinical Laboratory Techniques/methods , Coronavirus Infections/epidemiology , Female , Humans , Incidence , Infant , Infant, Newborn , Male , Middle Aged , Molecular Diagnostic Techniques , Pandemics , Pneumonia, Viral/epidemiology , RNA, Viral/analysis , Real-Time Polymerase Chain Reaction , Retrospective Studies , Sex Factors , Young Adult
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